NM_015980.5:c.*369A>T

Variant names:

• chr5-174107874-A-T
• rs4457100
• NM_015980.5:c.*369A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_015980.5(NSG2):​c.*369A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: NSG2 NM_015980.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.796
• Publications: 10 publications found

Genes affected

NSG2 (HGNC:24955): (neuronal vesicle trafficking associated 2) Predicted to enable clathrin light chain binding activity. Predicted to be involved in clathrin coat assembly and endosomal transport. Located in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NSG2	NM_015980.5	c.*369A>T		3_prime_UTR_variant	Exon 5 of 5	ENST00000303177.8	NP_057064.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NSG2	ENST00000303177.8	c.*369A>T		3_prime_UTR_variant	Exon 5 of 5	1	NM_015980.5	ENSP00000307722.3
NSG2	ENST00000521146.1	n.786A>T		non_coding_transcript_exon_variant	Exon 3 of 3	2
NSG2	ENST00000521959.5	n.830A>T		non_coding_transcript_exon_variant	Exon 4 of 4	2
NSG2	ENST00000521585.5	c.213+43559A>T		intron_variant	Intron 3 of 4	4		ENSP00000429863.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 249666 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 139444

African (AFR) AF: 0.00 AC: 0 AN: 6756

American (AMR) AF: 0.00 AC: 0 AN: 18934

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 6598

East Asian (EAS) AF: 0.00 AC: 0 AN: 9706

South Asian (SAS) AF: 0.00 AC: 0 AN: 47008

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10340

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1928

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 136280

Other (OTH) AF: 0.00 AC: 0 AN: 12116

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.6
DANN	Benign	0.62
PhyloP100		0.80

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4457100; hg19: chr5-173534877;